Analysis info and important parameters

rsfMRI data Parameters:

rsfMRI: mr_pcorr.txt file
Z norm before load: False
upsampling: UP

ML Parameters:

Z norm in glmnet: True
W: constant declarative=0.5, procedural=0.5 (because of UP sampling)
Hyperparameter tuning: nfolds = length(Y)
Model evaluation: nfolds = 20

Nested CV Parameters

Betas: |mean beta| > 0.05

iGraph Parameters

connectom betas: NOT nested beta
connection counts (duplicates): YES

Load subject data

power2011 <- read_csv("../bin/power_2011.csv", 
                      col_types = cols(ROI=col_double(),
                                       X = col_double(),
                                       Y = col_double(),
                                       Z = col_double(),
                                       Network = col_double(),
                                       Color = col_character(),
                                       NetworkName = col_character())) %>%
  dplyr::select(ROI, X, Y, Z, Network, Color, NetworkName)

Create the Group-Level Regressor Matrix \(X\)

We now need to load the group level data. In essence, to corresponds to create a matrix X in which every individual is a row and every columns is a different ROI-to-ROI connection.

SKIP <- TRUE
if (SKIP){
  load("./__cache__/C_UP.RData")
  # color setup
  colors <- factor(power2011$Color)
  levels(colors) <-  c(brewer.pal(name="Set3", n = 12), brewer.pal(name="Set1", n = 9))[1:14]
  power2011$Color <- as.character(colors)
  #df.UP <- read_csv("./__cache__/REST1_SES01_MR_PCORR_UP_2022FEB_subj.csv")
  #C <- dfX.UP %>% dplyr::select(-HCPID) %>% as.matrix()
  #C <- apply(C, 2, FUN=as.numeric)
  #n <- dim(C)[[1]]
} else {
  NOFLY <- c()
  SUBJS <- c()
  cols <- outer(power2011$ROI, power2011$ROI, function(x, y) {paste(x, y, sep="-")})
  cols %<>% as.vector
  
  connection <- function(x, y) {
    paste(min(x, y), max(x, y), sep="-")
  }
  
  vconnection <- Vectorize(connection)
  
  Mode <- function(x, na.rm=F) {
    if (na.rm) {
      x = x[!is.na(x)]
    }
    ux <- unique(x)
    return(ux[which.max(tabulate(match(x, ux)))])
  }
  
  reduced_power2011 <- power2011 %>% 
    dplyr::select(Network, NetworkName) %>%
    group_by(Network) %>%
    summarize(Network = mean(Network), NetworkName = Mode(NetworkName))
  
  connection_name <- function(x, y) {
    first <- min(x, y)
    second <- max(x, y)
    paste(reduced_power2011 %>% filter(Network == first) %>% dplyr::select(NetworkName) ,
          reduced_power2011 %>% filter(Network == second) %>% dplyr::select(NetworkName),
          sep="-")
    
  }
  
  vconnection_name <- Vectorize(connection_name)
  
  connection_name2 <- function(x, y) {
    first <- min(x, y)
    second <- max(x, y)
    paste(reduced_power2011$NetworkName[reduced_power2011$Network == first],
          reduced_power2011$NetworkName[reduced_power2011$Network == second],
          sep="-")
    
  }
  
  vconnection_name2 <- Vectorize(connection_name2)
  
  
  nets <- outer(power2011$Network, power2011$Network, vconnection)
  nets %<>% as.vector
  netnames <- outer(power2011$Network, power2011$Network, vconnection_name2)
  netnames %<>% as.vector
  
  
  n <- length(grep("sub-*", dir("./connectivity_matrix/REST1")))
  C <- matrix(data = rep(0, length(cols)*n), nrow =  n)
  
  j <- 1
  
  R <- NULL
  PR <- NULL
  
  for (sub in dir("./connectivity_matrix/REST1")[grep("sub-*", dir("./connectivity_matrix/REST1"))]) {
    SUBJS %<>% c(strsplit(sub, "-")[[1]][2])
    M <- paste("./connectivity_matrix/REST1", 
               sub, 
               "ses-01/mr_pcorr.txt", sep="/") %>%
      read_csv(skip = 1,
               col_names = F,
               col_types = cols(
                 .default = col_double(),
                 X1 = col_character()
               )) %>%
      as.matrix() 
    v <- as_vector(M[,2:265])  # v spreads M column-wise. M is symmetrical, so it should not matter, but better not risk it
    C[j,] <- v
    if (length(v[is.na(v)]) > 0) {
      print(paste("NA detected in sub", sub))
      NOFLY %<>% c(sub)  # Addes sub to NOFLY list
    }
    
    j <- j + 1
  }
  C <- apply(C, 2, FUN=as.numeric)
}

Define the Networks

NOI <- c(
  "Uncertain",
  "Sensory/somatomotor Hand",
  "Sensory/somatomotor Mouth",
  "Cingulo-opercular Task Control",
  "Auditory",
  "Default mode",
  "Memory retrieval?",
  "Ventral attention",
  "Visual",
  "Fronto-parietal Task Control",
  "Salience",
  "Subcortical",
  "Cerebellar",
  "Dorsal attention"
)

COI <- outer(NOI, 
             NOI, 
             function(x, y) {paste(x, y, sep="-")}) %>% as.vector()

The first censor vector simply removes the redundant columns (since the connectivity from A to B is the same as the connectivity of B to A) and the self-correlations:

censor <- outer(power2011$ROI, 
                power2011$ROI, 
                function(x, y) {x < y}) %>% as.vector()

The second censor vector removes unlikely functional connections: Those with a partial correlation value \(|r| < 0.05|\).

censor2 <- colMeans(C) %>% abs() > 0.05

Now, we combine the censor vectors in a tibble that contains all of the relevant information about each column in C.

order <- tibble(index = 1:length(nets), 
                network = nets, 
                network_names = netnames,
                connection = cols, 
                censor=censor,
                censor2 = censor2)
order %<>% arrange(network)

And we remove all entries for each a censor vector is FALSE (we also create a grouping factor G, in case in the future we want to use Group Lasso).

I <- order %>%
  filter(censor == TRUE) %>%
  filter(censor2 == TRUE) %>%
  filter(network_names %in% COI) %>%
  dplyr::select(index) 

G <- order %>%
  filter(censor == TRUE) %>%
  filter(network_names %in% COI) %>%
  dplyr::select(network) 
# G is the real grouping factor for Lasso!

As a last step, we create the “real” regressor matrix \(X\), which is the proper subset of \(C\) after removing all of the censored columns. Also, we need to load the dependent variable. In this case, it is a binary variable that determines which strategy model best fits the behavioral data of an individual, whether it is the “memory” strategy (\(Y = 1\)) or the “procedural” strategy (\(Y = 2\)).

X <- C[,as_vector(I)]

dvs <- read_csv("../actr-models/model_output/MODELLogLikelihood.csv",
                col_types = cols(
                  .default = col_double(),
                  HCPID = col_character(),
                  best_model = col_character()
                )) %>% 
  dplyr::select(HCPID, best_model) %>%
  arrange(HCPID)

Now we select only the rows of \(X\) and the values of \(Y\) for which we have both rsfMRI and model data.

The dimension of X is: 230, 628

Y <- dfY.UP$best_model1

Finally, we transform the dependent variable \(Y\) into a binary numeric variable with values \((0, 1)\), so that we can use logistic regression.

Y <- as.numeric(as.factor(Y)) - 1

Quality and Characteristics of \(X\) and \(Y\)

Let’s do some visualization and analysis of our indepedenent and dependet variables, just to ensure there are no obvious problems.

Collinearity of Connectivity Regressors \(X\)

The regressors \(X\) is certainly multi-collinear; that is a consequence of having a large number of predictors \(p > n\), which, in turn, is one of the reasons why we are using Lasso. Too much collinearity, however, could be really bad and push Lasso towards selecting non-optimal regressors. To gather a sense of how much collinearity we have, we can plot the distribution of correlations among regressors:

corX <- cor(X)
distCor <- as_vector(corX[lower.tri(corX, diag = F)])
distTibble <- as_tibble(data.frame(R=distCor))

ggplot(distTibble, aes(x=R)) +
  geom_histogram(col="white", alpha=0.5, binwidth = 0.05) +
  theme_pander() +
  ylab("Number of Correlations") +
  xlab("Correlation Value") +
  ggtitle("Distribution of Correlation Values Between Regressors")

All in all, the collinearity is not that bad—all regressors are correlated at \(|r| < 0.25\), and most of them are correlated at \(|r| < 0.1\), with a peak at \(r = 0\).

Distribution of Classes

And now, let’s visualize the histogram of the dependent variable we are trying to predict:

dependent <- as_tibble(data.frame(strategy=dvs$best_model))

ggplot(dependent, aes(x = factor(strategy), fill=factor(strategy))) +
  geom_bar(col="white", alpha=0.5, width = .5) +
  scale_fill_nejm() +
  xlab("Strategy") +
  ylab("Number of Participants") +
  scale_x_discrete(labels=c( "m1" = "Declarative",  "m2" = "Procedural")) +
  ggtitle("Distribution of Strategy Use") +
  theme_pander() +
  theme(legend.position = "none")

Because the classes are not equally distributed, and participants are more likely to use the memory strategy (\(Y=0\)) than the procedural one (\(Y = 1\)), we would need to adjust the weights of our Lasso model.

Machine-Learning with Lasso

Cross-Validation

We can now define the lasso model. We will use the elastic net approach with \(\alpha = 0\) to generate a pure lasso model. The model will use a binomial (i.e., logistic) regression and will measure the cross-validation error as class misalignment.

To analyze the data, we will use Lasso, a statistical learning system based on penalized regression.

Most of the entries in our \(Y\) vector are coded as “0” (i.e., most participants use the memory strategy), which creates an imbalance. We are going to create an appropriate set of weights so that the two classes are balanced.

W <- Y
W[W == 0] <- mean(Y)
W[W == 1] <- (1-mean(Y))

fit <- glmnet(y = Y,
              x = X,
              alpha=1,
              weights = W,
              family = "binomial",
              type.measure = "class",
              standardize = T
)

To choose the optimal value of \(\lambda\) in Lasso, we will examine the cross-validation error during a LOO cross-validation.

fit.cv <- cv.glmnet(y = Y,
                    x = X,
                    alpha=1,
                    family = "binomial",
                    weights = W,
                    type.measure = "class",
                    standardize=T,
                    nfolds=length(Y),
                    grouped = F
)

Now, let’s look at the cross-validation error profile.

plot(fit.cv)

The profile has the characteristic U-shape or increasing curve, with more error as \(\lambda\) increases. As recommended by Tibishirani, we will select the “lambda 1SE” value, which is the largest \(\lambda\) value that does not differ by more tha 1 SE from the \(\lambda\) value that gives us the minimum cross validation error. This guarantees the maximum generalizability.

We can also visualize the profile of the beta weights of each connection for different values of \(\lambda\).

plot(fit, sub="Beta Values for Connectivity") 
L1norm <- sum(abs(fit$beta[,which(fit$lambda==fit.cv$lambda.1se)]))
abline(v=L1norm, lwd=2, lty=2)

And now, plot prettier version

lasso_df <- as_tibble(data.frame(lambda=fit.cv$lambda, 
                                 error=fit.cv$cvm, 
                                 sd=fit.cv$cvsd))

ggplot(lasso_df, aes(x=lambda, y=error)) +
  geom_line(aes(col=error), lwd=2) +
  scale_color_viridis("Error", option = "plasma") +
  geom_ribbon(aes(ymin=error -sd, ymax=error + sd), alpha=0.2,fill="blue") +
  xlab(expression(lambda)) +
  ylab("Cross-Validation Error") +
  ggtitle(expression(paste(bold("Cross Validation Error Across "), lambda))) +
  geom_vline(xintercept = lasso_df$lambda[lasso_df$error==min(lasso_df$error)]) +
  theme_pander() +
  theme(legend.position="right")

The min \(\lambda_{min}\) is 0.0398572, The 1se min \(\lambda_{min}\) is 0.0437432

Examining the Predictive Connectome

Let’s have a better look at the relevant connections that survive the Lass penalty at the value of \(\lambda_{min} + 1 SE\). We start by saving these connections in a tibble, and saving the data on a file for later use.

betas <- fit$beta[, which(fit$lambda==fit.cv$lambda.1se)]
conn_betas <- as_tibble(data.frame(index=I$index, Beta=betas))
connectome <- order %>%
  filter(index %in% I$index) %>%
  inner_join(conn_betas) %>%
  dplyr::select(-censor2) %>%
  filter(Beta != 0) %>%
  
  # reformat connectome
  separate(connection, c("connection1", "connection2"))%>%
  separate(network, sep = "-", c("network1", "network2"), remove = F) %>%
  #filter(str_detect(network, pattern = "-1-")) %>%
  mutate(network1 = ifelse(str_detect(network, pattern = "-1-"), -1, network1)) %>%
  mutate(connection_type = ifelse(network1==network2, "Within", "Between")) %>%
  arrange(index)


# HARD CODE
connectome[connectome$network=="-1-5","network2"] <- "5"
connectome[connectome$network=="-1-7","network2"] <- "7"
connectome[connectome$network=="-1--1","network2"] <- "-1"
connectome[connectome$network=="-1-11","network2"] <- "11"
connectome[connectome$network=="-1-12","network2"] <- "12"
connectome[connectome$network=="-1-13","network2"] <- "13"

In sum, connectome has 52 non-zero connections, 28 positive beta, and 24 negative betas. We will use these betas for later brain connectivity analysis.

Model Evaluation

plot_prediction <- function(Y, Yp, title) {
wcomparison <- tibble(Observed = Y,
                    Predicted = Yp,
                    DiscretePredicted = ifelse(Yp < 0.5, 0, 1))
            
wcomparison %<>% mutate(Accuracy = ifelse(DiscretePredicted == Observed,
                                          "Correct", 
                                          "Misclassified")) %>% drop_na()
  
#rval <- floor(100*cor(Y, Yp))/100
aval <- round(100*nrow(dplyr::filter(wcomparison, Accuracy %in% "Correct")) / nrow(wcomparison),2)

p <- ggplot(wcomparison, aes(x=Predicted, y=Observed, 
                             col=Accuracy)) +
  geom_point(size=4, alpha=0.6, 
             position= position_jitter(height = 0.02)) +
  geom_abline(intercept = 0, slope = 1, 
              col="red",
              linetype="dashed") +
  scale_color_d3() +
  theme_pander() +

  theme(legend.position = "right") +
  guides(col=guide_legend("Classification")) +
  coord_fixed(xlim=c(0, 1), ylim=c(0, 1)) +
  annotate("text", x=0.3, y=0.7,
           label=paste("Accuracy (",
                       length(Y),
                       ") = ",
                       aval,
                       "%",
                       sep="")) +
  ylab("Observed Strategy") +
  xlab("Predicted Strategy") +
  ggtitle(paste("Predicted vs. Observation",title)) +
  theme(legend.position = "bottom")
  
  ggMarginal(p, 
             fill="grey", 
             alpha=0.75,
             type="density", #bins=13, 
             col="darkgrey",
             margins = "both")
}

plot_roc <- function(Y, Yp, title) {
  wcomparison <- tibble(Observed = Y,
                    Predicted = Yp,
                    DiscretePredicted = ifelse(Yp < 0.5, 0, 1))
            
  wcomparison %<>% mutate(Accuracy = ifelse(DiscretePredicted == Observed,
                                            "Correct", 
                                            "Misclassified")) %>% drop_na()
  wcomparison %<>% mutate(ROCPrediction = if_else(Predicted < 0.5, 0, 1))

  rocobj <- roc(wcomparison$Observed, wcomparison$ROCPrediction)
  
  g <- ggroc(rocobj, col="red") +
    geom_point(aes(y=rocobj$sensitivities, x=rocobj$specificities), col="red", size=4, alpha=.5) +
    ggtitle(paste("AUC ROC Curve", title, round(rocobj$auc[[1]], 2))) +
    xlab("Specificity (FPR)") + ylab("Sensitivity (TPR)") + 
    geom_segment(aes(x = 1, xend = 0, y = 0, yend = 1), color="grey", linetype="dashed") +
    theme_pander()
  
  g
}

plot_roc_slide <- function(Y, Yp, title) {
  wcomparison <- tibble(Observed = Y,
                    Predicted = Yp,
                    DiscretePredicted = ifelse(Yp < 0.5, 0, 1))
            
  wcomparison %<>% mutate(Accuracy = ifelse(DiscretePredicted == Observed,
                                            "Correct", 
                                            "Misclassified")) %>% drop_na()
  wcomparison %<>% mutate(ROCPrediction = if_else(Predicted < 0.5, 0, 1))
  curve <- NULL

  for (threshold in seq(0, 1, 0.01)) {
    subthreshold <- wcomparison %>%
      mutate(Prediction = ifelse(Predicted > 1, 1, Predicted)) %>%
      mutate(Prediction = ifelse(Prediction <= 0, 1e-204, Prediction)) %>%
      mutate(Prediction = ifelse(Prediction <= threshold, 0, 1)) %>%
      mutate(Accuracy = ifelse(Prediction == Observed, 1, 0)) %>%
      group_by(Observed) %>%
      summarise(Accuracy = mean(Accuracy))
    
    tnr <- subthreshold %>% 
      filter(Observed == 0) %>% 
      dplyr::select(Accuracy) %>%
      as.numeric()
    
    tpr <- subthreshold %>% 
      filter(Observed == 1) %>% 
      dplyr::select(Accuracy) %>%
      as.numeric()
    
    partial <- tibble(Threshold = threshold,
                      TNR = tnr,
                      TPR = tpr)
    if (is.null(curve)) {
      curve <- partial
    } else {
      curve <- rbind(curve, partial)
    }
  }
  
  s <- ggplot(arrange(curve, TPR), aes(x=TNR, y=TPR)) + 
    geom_point(size=2, col="red", alpha=0.5) + 
    geom_line(col="red") + 
    ylab("Sensitivity (True Positive Rate)") +
    xlab("Specificity (True Negative Rate)") +
    scale_x_reverse() +
    # ylim(0, 1) +
    # xlim(1, 0) +
    ggtitle("ROC Curve for Different Thresholds") +
    geom_abline(slope=1, intercept = 1, col="grey", linetype = "dashed") +
    theme_pander()
  s
}

# validation data misclassification error
fit.cv.accuracy <- 1-assess.glmnet(fit.cv, X, Y, weights = W, s="lambda.1se", family = "binomial")$class %>% as.vector()# best lambda cv error
fit.cv.auc <- assess.glmnet(fit.cv, X, Y, weights = W, s="lambda.1se", family = "binomial")$auc %>% as.vector()# best lambda cv error
  
# training data prediction probabilities
fit.cv.pred <- predict(fit.cv, newx = X, weights = W, s="lambda.1se", type="class", family = "binomial")%>% as.numeric()
fit.cv.predprob <- predict(fit.cv, newx = X, weights = W, s="lambda.1se", type="response", family = "binomial")%>% as.numeric()

Calculate training Accuracy score (0.9391304) and AUC score (0.9882042)

Predicted vs. Observed

plot_prediction(Y, fit.cv.predprob, "(Training)")

ROC

plot_roc(Y, fit.cv.predprob, "Training")

ROC Curve By Sliding Threshold

plot_roc_slide(Y, fit.cv.predprob, "Training")

Finally, we can visualize the table of connections

connectome %>%
  xtable() %>%
  kable(digits = 5) %>%
  kable_styling(bootstrap_options = c("striped", "hover"))

index	network	network1	network2	network_names	connection1	connection2	censor	Beta	connection_type
265	-1–1	-1	-1	Uncertain-Uncertain	1	2	TRUE	1.36879	Between
7938	1-1	1	1	Sensory/somatomotor Hand-Sensory/somatomotor Hand	18	31	TRUE	-0.15437	Within
15632	3-3	3	3	Cingulo-opercular Task Control-Cingulo-opercular Task Control	56	60	TRUE	0.99294	Within
18017	4-4	4	4	Auditory-Auditory	65	69	TRUE	-0.39604	Within
18274	3-4	3	4	Cingulo-opercular Task Control-Auditory	58	70	TRUE	-0.20923	Between
21995	-1-5	-1	5	Uncertain-Default mode	83	84	TRUE	-0.50766	Between
24368	5-5	5	5	Default mode-Default mode	80	93	TRUE	-0.90469	Within
24906	5-5	5	5	Default mode-Default mode	90	95	TRUE	1.20568	Within
24907	5-5	5	5	Default mode-Default mode	91	95	TRUE	3.09692	Within
26235	5-5	5	5	Default mode-Default mode	99	100	TRUE	-0.41467	Within
28059	5-5	5	5	Default mode-Default mode	75	107	TRUE	1.96747	Within
28323	5-5	5	5	Default mode-Default mode	75	108	TRUE	3.57538	Within
31534	5-5	5	5	Default mode-Default mode	118	120	TRUE	-1.30753	Within
32549	5-5	5	5	Default mode-Default mode	77	124	TRUE	-1.23344	Within
35205	5-6	5	6	Default mode-Memory retrieval?	93	134	TRUE	1.78357	Between
35469	5-6	5	6	Default mode-Memory retrieval?	93	135	TRUE	2.53235	Between
36007	5-5	5	5	Default mode-Default mode	103	137	TRUE	0.23319	Within
37613	5-7	5	7	Default mode-Visual	125	143	TRUE	-7.44176	Between
40807	7-7	7	7	Visual-Visual	151	155	TRUE	1.04365	Within
41075	7-7	7	7	Visual-Visual	155	156	TRUE	1.66648	Within
42390	7-7	7	7	Visual-Visual	150	161	TRUE	-0.77231	Within
42927	7-7	7	7	Visual-Visual	159	163	TRUE	11.55222	Within
43186	7-7	7	7	Visual-Visual	154	164	TRUE	-0.66595	Within
43694	6-7	6	7	Memory retrieval?-Visual	134	166	TRUE	-0.10121	Between
43715	7-7	7	7	Visual-Visual	155	166	TRUE	0.07205	Within
44501	7-7	7	7	Visual-Visual	149	169	TRUE	0.95431	Within
44514	7-7	7	7	Visual-Visual	162	169	TRUE	0.90955	Within
45566	7-7	7	7	Visual-Visual	158	173	TRUE	-0.51889	Within
45576	7-7	7	7	Visual-Visual	168	173	TRUE	-0.12955	Within
45810	8-11	8	11	Fronto-parietal Task Control-Ventral attention	138	174	TRUE	-1.97600	Between
46551	5-8	5	8	Default mode-Fronto-parietal Task Control	87	177	TRUE	-1.35795	Between
46564	5-8	5	8	Default mode-Fronto-parietal Task Control	100	177	TRUE	-0.39975	Between
46778	3-8	3	8	Cingulo-opercular Task Control-Fronto-parietal Task Control	50	178	TRUE	-4.06699	Between
47700	8-8	8	8	Fronto-parietal Task Control-Fronto-parietal Task Control	180	181	TRUE	0.56192	Within
48759	-1–1	-1	-1	Uncertain-Uncertain	183	185	TRUE	-3.70318	Between
49015	8-8	8	8	Fronto-parietal Task Control-Fronto-parietal Task Control	175	186	TRUE	0.46332	Within
52464	8-8	8	8	Fronto-parietal Task Control-Fronto-parietal Task Control	192	199	TRUE	1.31359	Within
53422	5-9	5	9	Default mode-Salience	94	203	TRUE	-2.18325	Between
54559	8-9	8	9	Fronto-parietal Task Control-Salience	175	207	TRUE	-1.51112	Between
55120	9-9	9	9	Salience-Salience	208	209	TRUE	-5.34940	Within
55500	3-9	3	9	Cingulo-opercular Task Control-Salience	60	211	TRUE	-5.43483	Between
59358	10-10	10	10	Subcortical-Subcortical	222	225	TRUE	1.56887	Within
60516	3-10	3	10	Cingulo-opercular Task Control-Subcortical	60	230	TRUE	0.43360	Between
61041	3-10	3	10	Cingulo-opercular Task Control-Subcortical	57	232	TRUE	0.70970	Between
62630	4-11	4	11	Auditory-Ventral attention	62	238	TRUE	2.92570	Between
63756	-1-11	-1	11	Uncertain-Ventral attention	132	242	TRUE	0.25863	Between
64071	-1-13	-1	13	Uncertain-Cerebellar	183	243	TRUE	3.16668	Between
64335	-1-13	-1	13	Uncertain-Cerebellar	183	244	TRUE	0.14462	Between
67242	1-8	1	8	Sensory/somatomotor Hand-Fronto-parietal Task Control	186	255	TRUE	1.29517	Between
68303	8-12	8	12	Fronto-parietal Task Control-Dorsal attention	191	259	TRUE	-0.44701	Between
68814	8-12	8	12	Fronto-parietal Task Control-Dorsal attention	174	261	TRUE	0.87236	Between
69218	3-12	3	12	Cingulo-opercular Task Control-Dorsal attention	50	263	TRUE	3.03705	Between

Stability of Estimated Beta Weights

And now, let’s visualize the beta weights of the connections: num connections=52

ggplot(connectome, aes(x = reorder(connection, Beta), y = Beta)) +
  geom_point(aes(col=Beta), alpha=.5, 
             size=2,
             position = position_jitter(height = 0, width = 0.3)) +
  stat_summary(fun.data = "mean_sdl", geom="point", fill="black", alpha=1, size=1) +
  scale_color_gradient2(low = "dodgerblue",
                        mid = "wheat",
                        high = "red2",
                        midpoint = 0) +
  scale_x_discrete(labels = 
                     paste(connectome$network_names, 
                           " (", 
                           connectome$connection,
                           ")", sep="")) +
  ggtitle(paste("Connection Weights Across Cross-Validation:", dim(connectome)[[1]])) +
  ylab(expression(paste(beta, " value"))) +
  xlab("Connection") +
  geom_hline(yintercept = 0, col="grey") +
  stat_summary(fun.data = "mean_cl_boot", 
               col="black", geom="errorbar", width=1) +
  scale_color_viridis(option="plasma", begin=0.2, end=0.9) +
  theme_pander() +
  theme(axis.text.y = element_text(angle=0, hjust=1),
        legend.position = "NA") +
  #ylim(-3, 3) +
  coord_flip()

connectome %>% 
  mutate(beta_sign = ifelse(Beta >0, "+", "-")) %>%
  ggdotchart(x = "network_names", y = "Beta",
           color = "beta_sign",                                # Color by groups
           palette = c("steelblue", "tomato"), # Custom color palette
           rotate = TRUE,
           facet.by = "connection_type", 
           sort.by.groups = F,
           sort.val = "desc",          # Sort the value in descending order
           sorting = "descending",                       # Sort value in descending order
           add = "segments",                             # Add segments from y = 0 to dots
           add.params = list(color = "lightgray", size = 2), # Change segment color and size
           group = "connection_type",                                # Order by groups
           dot.size = 3,                                 # Large dot size
           #label = round(connectome$Beta,2),                        # Add mpg values as dot labels
           #font.label = list(color = "white", size = 9,
           #                  vjust = 0.5),               # Adjust label parameters
           #group = "cyl",
           #y.text.col = TRUE,
           title = paste("Lasso Connection Weights:", dim(connectome)[[1]]),
           ggtheme = theme_pander()) +
  geom_hline(yintercept = 0, linetype = 2, color = "black")

Statistical analysis of Network Distribution

Lasso vs. Power

subsetPower <- filter(power2011,
                      NetworkName %in% NOI)
noi_stats <- subsetPower %>%
  group_by(NetworkName, Color) %>%
  summarise(N=length(Color)/dim(subsetPower)[1]) %>%
  add_column(Source="Power")

lROIs <- unique(c(connectome$connection1, connectome$connection2))

rois <- power2011[lROIs,]
roi_stats <- rois %>%
  group_by(NetworkName, Color, .drop = F) %>%
  summarise(N=length(Color)/length(lROIs)) %>%
  add_column(Source="Lasso") 


roi_stats <- roi_stats %>% 
  right_join(noi_stats %>% dplyr::select(NetworkName, Color), on = c("NetworkName", "Color")) %>%
  mutate(N = ifelse(is.na(N), 0, N), Source="Lasso") %>%
  arrange(NetworkName)

total_stats <- rbind(noi_stats, roi_stats)

ggplot(total_stats, aes(x="", y=N, fill=NetworkName)) +
  geom_bar(stat = "identity", col="white", width=1) +
  facet_grid(~Source, labeller = label_both) +
  coord_polar("y", start=0) +
  scale_y_continuous(labels = scales::percent_format(accuracy = 2L)) +
  scale_fill_manual(values = unique(power2011$Color)) +
  #scale_fill_viridis(discrete = T) +
  #scale_fill_ucscgb() +
  ylab("") +
  xlab("") +
  ggtitle("Distriution of ROI") +
  geom_text_repel(aes(label=percent(N, .1)), col="black", 
            position=position_stack(vjust=.01), size=3)+
  theme_pander() +
  guides(fill=guide_legend(ncol=2)) +
  theme(legend.position = "bottom")

#ggbarplot(total_stats, x="NetworkName", y="N", facet.by = "Source", fill = "NetworkName", color = "white",
#          merge = T, label = F,
#          ) +
#  coord_polar("y", start=0)

chisq.test(roi_stats$N*length(lROIs), p = noi_stats$N)

## 
##  Chi-squared test for given probabilities
## 
## data:  roi_stats$N * length(lROIs)
## X-squared = 13.615, df = 13, p-value = 0.4015

Lasso vs. Power:

Between vs. Within

net_from <- function(s) {as.character(strsplit(s, "-")[[1]][1])}
net_to <- function(s) {as.character(strsplit(s, "-")[[1]][2])}

vnet_from <- Vectorize(net_from)
vnet_to <- Vectorize(net_to)

connectivity <- function(s) {
  if (net_from(s) == net_to(s)) {
    "Within"
  } else {
    "Between"
  }
}

vconnectivity <- Vectorize(connectivity)
coi <- order %>%
  filter(censor == TRUE) %>%
  filter(network_names %in% COI) 

coi$from <- vnet_from(coi$network_names)
coi$to <- vnet_to(coi$network_names)
coi$connection_type <- vconnectivity(coi$network_names)

coi_stats <- coi %>% 
  group_by(connection_type) %>% 
  summarise(N=length(index), P=length(index)/dim(coi)[1]) %>%
  add_column(Source = "Power et al. (2011)")

connectome$connection_type <- vconnectivity(connectome$network_names)
connectome_stats <- connectome %>%
  group_by(connection_type) %>% 
  summarise(N=length(index), P=length(index)/dim(connectome)[1]) %>%
  add_column(Source = "Lasso Analysis")

connect_stats <- rbind(connectome_stats, coi_stats)

ggplot(connect_stats, aes(x="", y=P, fill=connection_type)) +
  geom_bar(stat = "identity", col="grey", width=1) +
  facet_grid(~Source, labeller = label_both) +
  coord_polar("y", start=0) +
  scale_y_continuous(labels = scales::percent_format(accuracy = 2L)) +
  scale_fill_jama() +
  scale_color_jama() +
  ylab("") +
  xlab("") +
  ggtitle("Distribuction of Connectivity\n(Within/Between Networks)") +
  geom_text_repel(aes(label=percent(P, .1)), col="white",
            position=position_stack(vjust=1), size=3)+
  theme_pander() +
  theme(legend.position = "bottom")

chisq.test(connectome_stats$N, p=coi_stats$P)

## 
##  Chi-squared test for given probabilities
## 
## data:  connectome_stats$N
## X-squared = 87.815, df = 1, p-value < 2.2e-16

Nested Cross-Validation

NOTE: In this case, lambda is not same for each subject

N <- length(Y)
P <- ncol(X)
betas <- matrix(rep(0, P * N), nrow = N)
Yp <- rep(0, N)
minF = 1
#X <- atanh(X)  ## ??? WHY USE atanh
dfX <- as.data.frame(cbind(Y, X))
for (i in 1:N) {
  Ytrain <- Y[-i]
  Xtrain <- X[-i,]
  Wtrain <- W[-i]
  # fit <- ncvreg
  fit <- glmnet(y = Ytrain,
                x = Xtrain,
                weights = Wtrain,
                alpha = 1,
                family = "binomial",
                type.measure ="class",
                standardize = T
  )
  
  fit.cv <- cv.glmnet(y = Ytrain,
                      x = Xtrain,
                      alpha=1,
                      weights=Wtrain,
                      #penalty="SCAD",
                      family = "binomial",
                      type.measure = "class",
                      standardize=T,
                      grouped=F,
                      nfolds=20
                      #nfolds=length(Ytrain)
  )
  
  
  lambda <- fit.cv$lambda.min
  nzero <- fit.cv$nzero[which(fit.cv$lambda == fit.cv$lambda.min)]
  
  if (fit.cv$nzero[which(fit.cv$lambda == fit.cv$lambda.1se)] > 0) {
    lambda <- fit.cv$lambda.1se
    nzero <- fit.cv$nzero[which(fit.cv$lambda == fit.cv$lambda.1se)]
  }
  
  if (nzero < minF) {
    # If no features, select a less-generalizable lambda
    lambda <- fit.cv$lambda[which(fit.cv$nzero >= minF)[1]]
  } 
  
  B <- fit$beta[,which(fit$lambda==lambda)]
  #B <- coef(fit.cv, s=lambda) %>% as.matrix()
  #B <- fit$beta[,which(fit$lambda==fit$lambda[60])]
  #print(B)
  #print(fit.cv$lambda.min)
  #plot(fit.cv)
  if (length(B[B!=0])) {
    #print(c(i, length(B[B!=0])))
    dfX <- data.frame(cbind(Y, X[, B != 0]))
    #lmod<-lm(Y ~ . + 1, data=dfX[-i,])
    #print(lmod)
    #Xtest <- dfX[i,-1]
    #yp <- lmod$coefficients[1] + sum(B*X[i,])# predict on test data
    yp <- predict(fit.cv, newx = X[-i,], s=lambda, type="response")
    assess.glmnet(fit.cv, X[-i,], Y[-i], weights = W[-i], s=fit.cv$lambda.min, family = "binomial")$class # best lambda cv error
    assess.glmnet(fit.cv, X[-i,], Y[-i], weights = W[-i], s=fit.cv$lambda.min, family = "binomial")$auc # best lambda cv auc
    assess.glmnet(fit, X[-i,], Y[-i], weights = W[-i], s=fit.cv$lambda.min, family = "binomial")$class # best lambda cv error = same as first
    
  } else {
    yp <- mean(Ytrain)
  }
  betas[i,] <- B
  Yp[i] <- yp
}

set.seed(0)
#dfX <- data.frame(cbind(Y, X[,betas != 0]))
nrounds <- 200
nfolds <- 20
ntest <- 30
nP <- ncol(X)
nO <- nrow(X)
# Training log0
Yp.train <- matrix(rep(NA, nO * nO),  ncol = nO) %>% as.data.frame()  # Vector of zeros the size of 176 x 176 

# Prediction log
nested.train.Yp <- matrix(rep(NA, nO * nrounds),  ncol = nrounds)
nested.train.Ypp <- matrix(rep(NA, nO * nrounds),  ncol = nrounds)
nested.test.Yp <- matrix(rep(NA, nO * nrounds),  ncol = nrounds)
nested.test.Ypp <- matrix(rep(NA, nO * nrounds),  ncol = nrounds)

### Score log
nested.train.errorscore <- c()
nested.train.aucscore <- c()
nested.test.errorscore <- c()
nested.test.acuscore <- c()

### Coefs log
Xcoef <- matrix(rep(NA, nP * nrounds),  ncol = nrounds) # Matrix of zeros the dimensions of X (645 x 176)

### Best Lambda log
nested.lambdas <- c()

#colnames(Xco) <- paste("s", 1:numO, sep="")
#rownames(Xco) <- paste("b", 1:numP, sep="")
for(i in 1:nrounds) {
  tryCatch({
    #print(i)
    #if (i==7) stop("Urgh, the iphone is in the blender !")
  itest <- sample(seq(length(Y)), ntest, replace=FALSE)
  #itest <- seq(i, i+2) %>% as.integer()
  #if (i+2==length(Y)) { break }
  iW <- Y[-itest]
  iW[iW == 0] <- mean(Y[-itest])
  iW[iW == 1] <- (1-mean(Y[-itest]))
  
  ilasso <- glmnet(x=X[-itest, ], y=Y[-itest], 
                   alpha=1,
                   weights = iW,
                   family = "binomial", 
                   type.measure = "class",  
                   standardize=F)
  
  ilasso.cv <- cv.glmnet(x=X[-itest, ], y=Y[-itest], 
                        alpha=1,
                        weights=iW,
                        #penalty="SCAD",
                        family = "binomial",
                        type.measure = "class",
                        standardize=T,
                        grouped=F,
                        nfolds=nfolds)
  
  # define best lambda
  bestlambda <- fit.cv$lambda.min
  nested.lambdas <- c(nested.lambdas, bestlambda)
  
  # validation data misclassification error
  ilasso.cv.error <-assess.glmnet(ilasso.cv, X[-itest,], Y[-itest], weights = W[-itest], s=bestlambda, family = "binomial")$class %>% as.vector()# best lambda cv error
  ilasso.cv.auc <-assess.glmnet(ilasso.cv, X[-itest,], Y[-itest], weights = W[-itest], s=bestlambda, family = "binomial")$auc %>% as.vector()# best lambda cv error
  # training data prediction probabilities
  ilasso.cv.pred <- predict(ilasso.cv, newx = X[-itest,], weights = W[-itest], s=bestlambda, type="class", family = "binomial")%>% as.numeric()
  ilasso.cv.predprob <- predict(ilasso.cv, newx = X[-itest,], weights = W[-itest], s=bestlambda, type="response", family = "binomial")%>% as.numeric()
  
  # testing data misclassification error
  ilasso.test.error <-assess.glmnet(ilasso.cv, X[itest,], Y[itest], weights = W[itest], s=bestlambda, family = "binomial")$class %>% as.vector()# best lambda cv error
  ilasso.test.auc <-assess.glmnet(ilasso.cv, X[itest,], Y[itest], weights = W[itest], s=bestlambda, family = "binomial")$auc %>% as.vector()# best lambda cv error
  # training data prediction probabilities
  ilasso.test.pred <- predict(ilasso.cv, newx = X[itest,], weights = W[itest], s=bestlambda, type="class", family = "binomial")%>% as.numeric()
  ilasso.test.predprob <- predict(ilasso.cv, newx = X[itest,], weights = W[itest], s=bestlambda, type="response", family = "binomial")%>% as.numeric()
  
  # coeff
  B <- coef(ilasso.cv, s=bestlambda)[-1,] # do not keep intercept
  
  ### LOG Score
  nested.train.errorscore <- c(nested.train.errorscore, ilasso.cv.error)
  nested.train.aucscore <- c(nested.train.aucscore, ilasso.cv.auc)
  nested.test.errorscore <- c(nested.test.errorscore, ilasso.test.error)
  nested.test.acuscore <- c(nested.test.acuscore, ilasso.test.auc)
  
  ### LOG Coefs
  Xcoef[,i] <- B
  
  ### LOG Prediction
  nested.train.Yp[-itest,i] <- ilasso.cv.pred
  nested.train.Ypp[-itest,i] <- ilasso.cv.predprob
  nested.test.Yp[itest,i] <- ilasso.test.pred
  nested.test.Ypp[itest,i] <- ilasso.test.predprob

  }, error=function(e){
    print(paste('i=', i, "Uhhh, error\n"))
  })
}

Visualize Prediction vs. Observed on Training and Testing data ’ The Yp is calcualted by averaged across each round

Predicted vs. Observed

plot_prediction(Y, apply(nested.train.Ypp, 1, mean, na.rm=T), "(Training)")

plot_prediction(Y, apply(nested.test.Ypp, 1, mean, na.rm=T), "(Testing)")

ROC

plot_roc(Y, apply(nested.train.Ypp, 1, mean, na.rm=T), "(Training)")

plot_roc(Y, apply(nested.test.Ypp, 1, mean, na.rm=T), "(Testing)")

ROC By Sliding Threshold

plot_roc_slide(Y, apply(nested.train.Ypp, 1, mean, na.rm=T), "(Training)")

plot_roc_slide(Y, apply(nested.test.Ypp, 1, mean, na.rm=T), "(Testing)")

### LOG Score
nested.df <- data.frame(score=1-nested.train.errorscore, data_type="train", score_type="Accuracy", rounds = seq(1:nrounds)) %>%
  rbind(data.frame(score=1-nested.test.errorscore, data_type="test", score_type="Accuracy", rounds = seq(1:nrounds))) %>%
  rbind(data.frame(score=nested.train.aucscore, data_type="train", score_type="AUC", rounds = seq(1:nrounds))) %>%
  rbind(data.frame(score=nested.test.acuscore, data_type="test", score_type="AUC", rounds = seq(1:nrounds))) 
  
ggboxplot(data=nested.df, x="data_type" , y="score", 
          color = "data_type", #fill = "score_type", 
          facet.by = "score_type", add = "jitter") +
  geom_hline(yintercept = 0.5, col = "gray", line_type=1) +
  ggtitle("Nested CV: AUC and Accuracy for both Training and Testing data") +
  ylim(0,1) +
  theme_pander()

The left skewed distribution of Betas is a good sign that betas do not change significantly across CV Folds

Xcoef.stats <- data.frame(beta.id=seq(1:dim(Xcoef)[[1]]),beta.mean=apply(Xcoef,1,mean),  beta.sd=apply(Xcoef,1,sd))%>% # 1=Row, 2=Col 
  filter(beta.mean!=0) %>%
  arrange(-beta.sd)

Xcoef.stats %>% 
  gghistogram("beta.sd", bins = 100, fill = "steelblue", color = "white") +
  ggtitle("Distribution of Coefficients SD across Nested CV-folds") +
  theme_pander()

Examining the Predictive Connectome

nested_beta_thresh <- 0.05

uB <- rowMeans(Xcoef)
conn_betas_nested <- as_tibble(data.frame(index=I$index, Beta=uB))
connectome_nested <- order %>%
  filter(index %in% I$index) %>%
  inner_join(conn_betas_nested) %>%
  dplyr::select(-censor2) %>%
  #filter(Beta != 0) %>%
  filter(Beta <= -nested_beta_thresh | Beta >= nested_beta_thresh) %>%

  # reformat connectome
  separate(connection, c("connection1", "connection2"))%>%
  separate(network, sep = "-", c("network1", "network2"), remove = F) %>%
  #filter(str_detect(network, pattern = "-1-")) %>%
  mutate(network1 = ifelse(str_detect(network, pattern = "-1-"), -1, network1)) %>%
  mutate(connection_type = ifelse(network1==network2, "Within", "Between")) %>%
  arrange(index)


# HARD CODE
connectome_nested[connectome_nested$network=="-1-5","network2"] <- "5"
connectome_nested[connectome_nested$network=="-1-7","network2"] <- "7"
connectome_nested[connectome_nested$network=="-1--1","network2"] <- "-1"
connectome_nested[connectome_nested$network=="-1-11","network2"] <- "11"
connectome_nested[connectome_nested$network=="-1-12","network2"] <- "12"
connectome_nested[connectome_nested$network=="-1-13","network2"] <- "13"

After applying threshold 0.05, the remaining number of connections (NESTED) is 113

Stability of Estimated Beta Weights

And now, let’s visualize the beta weights of the connections

ggplot(connectome_nested, aes(x = reorder(connection, Beta), y = Beta)) +
  geom_point(aes(col=Beta), alpha=.5, 
             size=2,
             position = position_jitter(height = 0, width = 0.3)) +
  stat_summary(fun.data = "mean_sdl", geom="point", fill="black", alpha=1, size=1) +
  scale_color_gradient2(low = "dodgerblue",
                        mid = "wheat",
                        high = "red2",
                        midpoint = 0) +
  scale_x_discrete(labels = 
                     paste(connectome_nested$network_names, 
                           " (", 
                           connectome_nested$connection,
                           ")", sep="")) +
  ggtitle(paste("Connection Weights Across Cross-Validation", dim(connectome_nested)[[1]])) +
  ylab(expression(paste(beta, " value"))) +
  xlab("Connection") +
  geom_hline(yintercept = 0, col="grey") +
  stat_summary(fun.data = "mean_cl_boot", 
               col="black", geom="errorbar", width=1) +
  scale_color_viridis(option="plasma", begin=0.2, end=0.9) +
  theme_pander() +
  theme(axis.text.y = element_text(angle=0, hjust=1),
        legend.position = "NA") +
  #ylim(-3, 3) +
  coord_flip()

connectome_nested %>% 
  mutate(beta_sign = ifelse(Beta >0, "+", "-")) %>%
  ggdotchart(x = "network_names", y = "Beta",
           color = "beta_sign",                                # Color by groups
           palette = c("steelblue", "tomato"), # Custom color palette
           rotate = TRUE,
           facet.by = "connection_type", 
           sort.by.groups = F,
           sort.val = "desc",          # Sort the value in descending order
           sorting = "descending",                       # Sort value in descending order
           add = "segments",                             # Add segments from y = 0 to dots
           add.params = list(color = "lightgray", size = 2), # Change segment color and size
           group = "connection_type",                                # Order by groups
           dot.size = 3,                                 # Large dot size
           #label = round(connectome$Beta,2),                        # Add mpg values as dot labels
           #font.label = list(color = "white", size = 9,
           #                  vjust = 0.5),               # Adjust label parameters
           #group = "cyl",
           #y.text.col = TRUE,
           title = paste("Lasso Connection Weights(Nested):", dim(connectome_nested)[[1]]),
           ggtheme = theme_pander()) +
  geom_hline(yintercept = 0, linetype = 2, color = "black")

Testing the validity of the Lasso model

Here, we will examine the quality of our Lasso model bu doing a series of tests.

Ablation test

In the ablation test, we remove all the connections with significant beta values, and check whether the results are still significant.

XX <- X[, conn_betas$Beta == 0]

fit_wo <- glmnet(y = Y,
                 x = XX,
                 alpha=1,
                 lambda = fit$lambda,
                 family = "binomial",
                 type.measure = "class",
                 weights = W,
                 standardize = T
)

fit_wo.cv <- cv.glmnet(y = Y,
                       x = XX,
                       alpha=1,
                       weights = W,
                       lambda = fit$lambda,
                       standardize=T,
                       type.measure = "class",
                       family = "binomial",
                       grouped=F,
                       nfolds=length(Y)
)

The model does converge, but its overall classification error is much higher.

plot(fit_wo, sub="Beta Values for Connectivity")

L1norm <- sum(abs(fit_wo$beta[,which(fit_wo$lambda==fit_wo.cv$lambda.1se)]))
abline(v=L1norm, lwd=2, lty=2)

It is useful to plot the two \(\lambda\)-curves (with and without the relevant connections) on the same plot.

lasso_df_wo <- tibble(lambda=fit_wo.cv$lambda, 
                   error=fit_wo.cv$cvm, 
                   sd=fit_wo.cv$cvsd)



lasso_df$Model <- "Full Model"
lasso_df_wo$Model <- "Without the Selected Connections"

lasso_uber <- rbind(lasso_df, lasso_df_wo)

ggplot(lasso_uber, aes(x = lambda, y = error, fill=Model)) +
  #scale_color_d3() +
  #scale_fill_d3()+
  geom_ribbon(aes(ymin = error - sd, 
                  ymax = error + sd), 
              alpha = 0.5,
              #fill="blue"
              ) +
  geom_line(aes(col=Model), lwd=2) +
  xlab(expression(lambda)) +
  ylab("Cross-Validation Error") +
  ggtitle(expression(paste(bold("Cross Validation Error Across "), lambda))) +
  geom_vline(xintercept = fit.cv$lambda.1se,
             linetype="dashed") +
  ylim(0,1) +
  theme_pander() +
  theme(legend.position="bottom")

Variance Inflation Factor

Then, we examine the Variance Inflation Factor (VIF). To calculate the VIF, we need to first create a linear model of the factor effects:

dfX <- data.frame(cbind(Y, X[, betas != 0]))
#dfX <- data.frame(cbind(Y, X[conn_betas[conn_betas$Beta!=0,]$index]))
mod<-lm(Y ~ . + 1, as.data.frame(dfX))

We can now calculate the VIF and turn the results into a tibble:

vifs <- vif(mod)
vifsT <- tibble(VIF = vifs)

And, finally, we can plot an histogram of the distribution of VIF values. VIFs values < 10 are considered non-collinear; VIFs values < 5 are great. All of our factors have VIF values that a re much smaller than 5, which implies that they are as close to a normal basis set as possible.

ggplot(vifsT, aes( x =VIF)) +
  geom_histogram(col="white", binwidth = 0.1, fill="blue", alpha=0.4) +
  theme_pander() +
  xlab("VIF Value") +
  ylab("Number of Predictors") +
  ggtitle("Distribution of Variance Inflation Factors")

Brain Network Analysis (Power)

A Matrix

To calculate the averaged corr matrix A

find the Fisher’s Z values of the corresponding Pearson correlation coefficients
Average them
Find the reverse Fisher’s Z transform of that average value.

C.z <- FisherZ(C)
C.zmean <- matrix(colMeans(C.z), nrow=264, ncol = 264)
A <- FisherZInv(C.zmean)
A.vec <- as.vector(A)

W Matrix

Calculate W from betas and A Matrix

library(circlize)

connectom2matrix <- function(connectome, w) {
  empty_mat <- matrix(0, 264, 264, dimnames = list(paste0("X", 1:264), paste0("X", 1:264))) 
  empty_mat[connectome$index] <- connectome$W
  return(empty_mat)
}

# convert a 264*264 matrix back to connectom df
matrix2connectom <- function(mat, connectome, col_name) {
  connectome$temp = mat[connectome$index]
  connectome <- rename(connectome, !!col_name := temp)
  return(connectome)
}

# make the matrix symmetric
make_symmetric <- function(m) {
  # lower.tri is 0.0
  m[lower.tri(m)] <- t(m)[lower.tri(m)]
  return(m)
}

power_atals <- power2011 %>% 
  rename(ROI.Name = ROI, x.mni=X, y.mni=Y, z.mni=Z, network=NetworkName) %>% 
  mutate(ROI.Name=as.integer(ROI.Name), index = as.integer(ROI.Name),
         x.mni=as.integer(x.mni), y.mni=as.integer(y.mni), z.mni=as.numeric(z.mni)) %>%
  dplyr::select(ROI.Name, x.mni, y.mni, z.mni, network, index)

check_atlas(power_atals)

NESTED <- FALSE

if(NESTED) {
  connectome_data <- connectome_nested
} else {
  connectome_data <- connectome
}

Wconnectome <- connectome_data %>%
  mutate(A = A.vec[connectome_data$index], W = A*Beta)
  #separate(connection, c("connection1", "connection2"))%>%
  #separate(network, sep = "-", c("network1", "network2"), remove = F) %>%
  #filter(str_detect(network, pattern = "-1-")) %>%
         #network1 = ifelse(str_detect(network, pattern = "-1-"), -1, network1)) %>%
  #mutate(connection_type = ifelse(network1==network2, "Within", "Between"))

if (!SKIP) {
  write_csv(Wconnectome, file="./__cache__/strategy_mr.csv")
}


W_mat <- matrix(0, ncol = 264, nrow = 264)
W_mat[Wconnectome$index] <- Wconnectome$W
W_mat <- make_symmetric(W_mat) #CHECKED correct W_mat

## TEST CODE
Wconnectome %>% filter(W>0) %>%
  group_by(connection_type) %>%
  count()

Wconnectome %>% filter(W>0 & connection_type=="Between") %>% arrange(-W)
W_mat[64071]

print_mat_colrow_names <- function(mdat, ind){
  k <- arrayInd(ind, dim(mdat))
  print(paste("rowname: ", rownames(mdat)[k[,1]]))
  print(paste("colname: ", colnames(mdat)[k[,2]]))
}

print_mat_colrow_names(W_mat, 64071)

Wconnectome %>% 
  mutate(W_sign = ifelse(W >0, "+", "-")) %>%
  ggdotchart(x = "network_names", y = "W",
           color = "W_sign",                                # Color by groups
           palette = c("steelblue", "tomato"), # Custom color palette
           rotate = TRUE,
           facet.by = "connection_type", 
           sort.by.groups = F,
           sort.val = "desc",          # Sort the value in descending order
           sorting = "descending",                       # Sort value in descending order
           add = "segments",                             # Add segments from y = 0 to dots
           add.params = list(color = "lightgray", size = 2), # Change segment color and size
           group = "connection_type",                                # Order by groups
           dot.size = 3,                                 # Large dot size
           #label = round(connectome$Beta,2),                        # Add mpg values as dot labels
           #font.label = list(color = "white", size = 9,
           #                  vjust = 0.5),               # Adjust label parameters
           #group = "cyl",
           #y.text.col = TRUE,
           title = paste("Lasso Connection W:", dim(connectome)[[1]]),
           ggtheme = theme_pander()) +
  geom_hline(yintercept = 0, linetype = 2, color = "black")

lwd_mat = matrix(1, nrow = nrow(W_mat), ncol = ncol(W_mat))
rownames(lwd_mat) = rownames(W_mat)
colnames(lwd_mat) = colnames(W_mat)
lwd_mat[W_mat > 0] = 2

border_mat = matrix(NA, nrow = nrow(W_mat), ncol = ncol(W_mat))
rownames(border_mat) = rownames(W_mat)
colnames(border_mat) = colnames(W_mat)
border_mat[W_mat > 0] = "black"
border_mat[W_mat < 0] = "gray"

chordDiagram(W_mat, link.lwd = lwd_mat, link.border = border_mat, scale = T, reduce = F)
circos.clear()

rownames(W_mat) = power_atals$network
colnames(W_mat) = power_atals$network

#col_fun = colorRamp2(range(W_mat), c("tomato", "steelblue"))


#sorted_net <- sort(power_atals$network)
#colors14 = c(brewer.pal(name="Set3", n = 12), brewer.pal(name="Set1", n = 9))[1:14]
#sorted_col <- c(brewer.pal(name="Set3", n = 12), brewer.pal(name="Set1", n = 9))[1:14]
              #c(brewer.pal(name="Set2", n = 8), 
              #  "darksalmon", "limegreen", "ligghtpink", "olivedrab", "navy", "mediumpurple", "maroon")
#rand_color(14)#c(brewer.pal(name="Set1", n = 9), brewer.pal(name="Set2", n = 9))[1:14]

png(filename = "./__cache__/figures1.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)
chordDiagram(W_mat, directional = FALSE, transparency = 0.5, self.link = 2  , symmetric = TRUE, scale = F, reduce = F,
             annotationTrack = c("grid", "axis"), #annotationTrackHeight = mm_h(c(8, 5)),
             grid.col = unique(power2011$Color), col = ifelse(W_mat>0, "tomato2", "#00000000"))
title("Declarative Network")

# Legend making
#legend("right",pch=20,legend=unique(colnames(W_mat)),
#       col=colors[unique(colnames(W_mat))],bty="n",
#       cex=1,pt.cex=3,border="black") # Set legend
circos.clear()

png(filename = "./__cache__/figures2.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)
chordDiagram(W_mat, directional = FALSE, transparency = 0.5, self.link = 2  , symmetric = TRUE, scale = F, reduce = F,
             annotationTrack = c("grid", "axis"),
             grid.col = unique(power2011$Color), col = ifelse(W_mat<0, "steelblue", "#00000000"))
title("Procedural Network")
circos.clear()

chordDiagram(x=W_mat, directional = FALSE, transparency = .5, self.link = 2, symmetric = TRUE, scale = T, reduce = F,
             grid.col = unique(power2011$Color), col = ifelse(W_mat>0, "tomato2", "steelblue"))
title("Network connections")

circos.clear()

##Network and node desciptives

Next, we will look at Graph properties of two networks

iGraph: Density

The proportion of present edges from all possible edges in the network.

# select cols
roi_links <- Wconnectome %>% dplyr::select(connection1, connection2, W, connection_type, network, network_names)
# rename cols
colnames(roi_links) <- c("from", "to", "weight", "connection_type", "network", "network_names")

roi_nodes <- power2011 %>% rename(id = ROI) %>%
  mutate(NetworkName=factor(NetworkName), 
         Color=factor(Color))
levels(roi_nodes$Color) <- sample(colors(T), 14) 

# create a graph
net <- graph_from_data_frame(d=roi_links, vertices=roi_nodes, directed=F) 
#g <- graph_from_adjacency_matrix(W_mat,, mode = "upper")

net.d <- net - E(net)[E(net)$weight<0]
net.p <- net - E(net)[E(net)$weight>0]

df.density <- data.frame("edge_density"=c(edge_density(net.d, loops=F), 
                            edge_density(net.p, loops=F),
                            edge_density(net, loops=F)), 
           "network" = factor(c("Declarative", "Procedural", "Full"), levels = c("Declarative", "Procedural", "Full")))

df.density %>% ggbarplot(x="network", y="edge_density", color = "white", fill=c("tomato", "steelblue", "gray"), width = 0.5, label = T, lab.nb.digits = 5) +
  theme_pander() + 
  ggtitle("Degree Edge Density")

iGraph: Diameter

A network diameter is the longest geodesic distance (length of the shortest path between two nodes) in the network. In igraph, diameter() returns the distance, while get_diameter() returns the nodes along the first found path of that distance.

# make negative weights to positive
net.p.abs <- net.p
E(net.p.abs)$weight <- E(net.p.abs)$weight * (-1)

# make negative weights to positive
net.abs <- net
E(net.abs)$weight[E(net.abs)$weight<0] <- E(net.abs)$weight[E(net.abs)$weight<0] * (-1)


df.diameter <- data.frame("diameter"=c(diameter(net.d, directed=F), 
                        diameter(net.p.abs, directed=F),
                        diameter(net.abs, directed=T)), 
           "network" = factor(c("Declarative", "Procedural", "Full"), levels = c("Declarative", "Procedural", "Full")))

df.diameter %>% ggbarplot(x="network", y="diameter", color = "white", fill=c("tomato", "steelblue", "gray"), width = 0.5, label = T, lab.nb.digits = 5) +
  theme_pander() + 
  ggtitle("Network Diameter")

#### iGraph: Centrality Degree

Centrality functions (vertex level) and centralization functions (graph level). The centralization functions return res - vertex centrality, centralization, and theoretical_max - maximum centralization score for a graph of that size. The centrality function can run on a subset of nodes (set with the vids parameter). This is helpful for large graphs where calculating all centralities may be a resource-intensive and time-consuming task.

Centrality is a general term that relates to measures of a node’s position in the network. There are many such centrality measures, and it can be a daunting task to wade through all of the different ways to measure a node’s importance in the network. Here, we will introduce just a few examples.

df.centrality <- data.frame("centr_degree"=c(centr_degree(net.d, normalized=T)$centralization, 
                        centr_degree(net.p, normalized=T)$centralization,
                        centr_degree(net, normalized=T)$centralization), 
           "network" = factor(c("Declarative", "Procedural", "Full"), levels = c("Declarative", "Procedural", "Full")))

df.centrality %>% ggbarplot(x="network", y="centr_degree", color = "white", fill=c("tomato", "steelblue", "gray"), width = 0.5, label = T, lab.nb.digits = 5) +
  theme_pander() + 
  ggtitle("Network Degree centrality ")

iGraph: Betweeness (Closeness)

Let’s now do the same for betweenness centrality, which is defined as the number of geodesic paths (shortest paths) that go through a given node. Nodes with high betweenness might be influential in a network if, for example, they capture the most amount of information flowing through the network because the information tends to flow through them. Here, we use the normalized version of betweenness.

Closeness (centrality based on distance to others in the graph) Inverse of the node’s average geodesic distance to others in the network.

df.sloseness <- data.frame("centr_clo"=c(centr_clo(net.d)$centralization, 
                        centr_clo(net.p)$centralization,
                        centr_clo(net)$centralization), 
           "network" = factor(c("Declarative", "Procedural", "Full"), levels = c("Declarative", "Procedural", "Full")))

df.sloseness %>% ggbarplot(x="network", y="centr_clo", color = "white", fill=c("tomato", "steelblue", "gray"), width = 0.5, label = T, lab.nb.digits = 5) +
  theme_pander() + 
  ggtitle("Network Closeness")

iGraph: Distances

df.distance <- data.frame("mean_distance"=c(mean_distance(net.d, directed=F), 
                        mean_distance(net.p, directed=F),
                        mean_distance(net, directed=F)), 
           "network" = factor(c("Declarative", "Procedural", "Full"), levels = c("Declarative", "Procedural", "Full")))

df.distance %>% ggbarplot(x="network", y="mean_distance", color = "white", fill=c("tomato", "steelblue", "gray"), width = 0.5, label = T, lab.nb.digits = 5) +
  theme_pander() + 
  ggtitle("Network Closeness")

iGraph: Assortativity

df.assortativity<- data.frame("assortativity_degree"=c(assortativity_degree(net.d, directed=F), 
                        assortativity_degree(net.p, directed=F),
                        assortativity_degree(net, directed=F)), 
           "network" = factor(c("Declarative", "Procedural", "Full"), levels = c("Declarative", "Procedural", "Full")))

df.assortativity %>% ggbarplot(x="network", y="assortativity_degree", color = "white", fill=c("tomato", "steelblue", "gray"), width = 0.5, label = T, lab.nb.digits = 5) +
  theme_pander() + 
  ggtitle("Network Assortativity Degree")

W in Brain connection

#colors <- factor(power_atals$network)
#levels(colors) <- colors14
#power_atals$colors <- as.character(temp)
check_atlas(power_atals)
x1 <- W_mat
x1[x1<0] <- 0


p1 <- brainconn(atlas=power_atals, conmat=x1, node.color = power2011$Color, view = "top",
          node.size = igraph::degree(net.d)*2.5, all.nodes = TRUE, 
          edge.color = "tomato",  edge.color.weighted = FALSE, scale.edge.width = c(1,3), edge.alpha = 0.6,
          label.edge.weight = F,  show.legend = F,
          background.alpha = .3) #+ ggtitle("Strategy Predictability: W")
p2 <- brainconn(atlas=power_atals, conmat=x1, node.color = power2011$Color, view = "left",
          node.size = igraph::degree(net.d)*2.5, all.nodes = TRUE, 
          edge.color = "tomato",  edge.color.weighted = FALSE, scale.edge.width = c(1,3), edge.alpha = 0.6,
          label.edge.weight = F,  show.legend = F,
          background.alpha = .3) #+ ggtitle("Strategy Predictability: W")
p3 <- brainconn(atlas=power_atals, conmat=x1, node.color = power2011$Color, view = "back",
          node.size = igraph::degree(net.d)*2.5, all.nodes = TRUE, 
          edge.color = "tomato",  edge.color.weighted = FALSE, scale.edge.width = c(1,3), edge.alpha = 0.6,
          label.edge.weight = F,  show.legend = F,
          background.alpha = .3) #+ ggtitle("Strategy Predictability: W")

x2 <- W_mat
x2[x2>0] <- 0

p4 <- brainconn(atlas=power_atals, conmat=x2*-10, node.color = power2011$Color, view = "top",
          node.size = igraph::degree(net.p)*2.5, all.nodes = TRUE, 
          edge.color = "steelblue",  edge.color.weighted = FALSE, 
          scale.edge.width = c(1,3), edge.alpha = 0.6,
          label.edge.weight = F,  show.legend = F,
          background.alpha = .3)  



p5 <- brainconn(atlas=power_atals, conmat=x2*-10, node.color = power2011$Color, view = "left",
          node.size = igraph::degree(net.p)*2.5, all.nodes = TRUE, 
          edge.color = "steelblue",  edge.color.weighted = FALSE, 
          scale.edge.width = c(1,3), edge.alpha = 0.6,
          label.edge.weight = F,  show.legend = F,
          background.alpha = .3) 

p6 <- brainconn(atlas=power_atals, conmat=x2*-10, node.color = power2011$Color, view = "back",
          node.size = igraph::degree(net.p)*2.5, all.nodes = TRUE, 
          edge.color = "steelblue",  edge.color.weighted = FALSE, 
          scale.edge.width = c(1,3), edge.alpha = 0.6,
          label.edge.weight = F,  show.legend = F,
          background.alpha = .3)

png(filename = "./__cache__/figures4.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)
p1

png(filename = "./__cache__/figures5.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)
p2

png(filename = "./__cache__/figures6.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)
p3

png(filename = "./__cache__/figures7.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)
p4

png(filename = "./__cache__/figures8.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)

p5

png(filename = "./__cache__/figures9.png",  bg = "transparent", width =500, height = 500, units = "px", res = 150)

p6

x1[,] <-1
brainconn(atlas=power_atals, conmat=x1, node.color = power2011$Color, view = "top",
          node.size = 2, all.nodes = TRUE, 
          edge.color = "tomato",  edge.color.weighted = FALSE, scale.edge.width = c(1,3), edge.alpha = 0.6,
          
          background.alpha = .3)

# Add a legend
legend(1, 95, legend=power_atals$network, 
       col=power2011$Color, lty=1:2, cex=0.8)

Distribution of connections

Look at the distribution of network in two groups

DUPLICATE <- TRUE

c1 <- Wconnectome %>% filter(W>0) %>% mutate(roi = as.integer(connection1)) %>% dplyr::select(roi) %>%  unlist()
c2 <- Wconnectome %>% filter(W>0) %>% mutate(roi = as.integer(connection2)) %>% dplyr::select(roi) %>%  unlist()


c3 <- Wconnectome %>% filter(W<0) %>% mutate(roi = as.integer(connection1)) %>% dplyr::select(roi) %>%  unlist()
c4 <- Wconnectome %>% filter(W<0) %>% mutate(roi = as.integer(connection2)) %>% dplyr::select(roi) %>%  unlist()


if (DUPLICATE) {
  c12 <- c(c1, c2)
  c34 <- c(c3, c4)
} else {
  c12 <- unique(c(c1, c2))
  c34 <- unique(c(c3, c4))
}

df.c1 <- power2011[c12,] %>%
  mutate(NetworkName = factor(NetworkName)) %>%
  count(NetworkName, name = "count", .drop = F)%>%
  right_join(power2011 %>% dplyr::select(NetworkName, Color) %>% distinct(), on="NetworkName") %>%
  mutate(count=as.integer(ifelse(is.na(count), 0, count))) %>%
  arrange(NetworkName)


# df.c1 %>%
#   ggplot(aes(x = count, y=NetworkName)) +
#   geom_col(aes(fill = NetworkName)) +
#   scale_fill_manual(values=colors14, guide = guide_legend(reverse = T)) +
#   #scale_x_reverse(limits = c(8,0)) +
#   theme_pander() + 
#   ggtitle("Declarative network", subtitle = "Distribution of connections") +
#   theme(legend.position = "right", axis.text.y = element_blank(), axis.title.y = element_blank(),
#         plot.title = element_text(size = 20),
#         axis.text = element_text(size = 20),
#         legend.title = element_text(size = 20),
#         legend.text = element_text(size = 20)) 

p7 <- ggbarplot(df.c1, x="NetworkName", y="count", fill = "NetworkName", color="white",
          palette = df.c1$Color, #order = "count", 
          rotate = TRUE, ggtheme = theme_pander(), position = position_dodge(preserve = "single"),
          title = "Distribution of connections") +
      scale_y_reverse(limits=c(14,0), breaks=c(0,5, 10, 15)) +
      #scale_fill_manual(values = sort(df.c1$NetworkName, decreasing = T)) +
      theme(legend.position = "right", axis.text.y = element_blank(), axis.title.y = element_blank(),
        plot.title = element_text(size = 20),
        axis.text = element_text(size = 20),
        legend.title = element_text(size = 20),
        legend.text = element_text(size = 20))
  
p7

# count number of networks included in
df.c2 <- power2011[c34,] %>%
  mutate(NetworkName = factor(NetworkName)) %>%
  count(NetworkName, name = "count", .drop = F) %>%
  right_join(power2011 %>% dplyr::select(NetworkName, Color) %>% distinct(), on="NetworkName") %>%
  mutate(count=ifelse(is.na(count), 0, count)) %>%
  arrange(NetworkName) 


# df.c2 %>%
#   ggplot(aes(x = count, y=NetworkName)) +
#   geom_col(aes(fill = NetworkName)) +
#   scale_fill_manual(values=colors14, guide = guide_legend(reverse = T)) +
#   theme_pander() + 
#   ggtitle("Procedural network", subtitle = "Distribution of connections") +
#   theme(legend.position = "right", axis.text.y = element_blank(), axis.title.y = element_blank(),
#         plot.title = element_text(size = 20),
#         axis.text = element_text(size = 20),
#         legend.title = element_text(size = 20),
#         legend.text = element_text(size = 20)) 


p8 <- ggbarplot(df.c2, x="NetworkName", y="count", fill = "NetworkName", color="white",
          palette = df.c1$Color, #order = "count", 
          rotate = TRUE, ggtheme = theme_pander(), 
          title = "Distribution of connections") +
  #scale_y_reverse() +
  scale_y_continuous(limits = c(0,15), breaks=c(0,5, 10, 15)) +
    theme(legend.position = "right", axis.text.y = element_blank(), axis.title.y = element_blank(),
        plot.title = element_text(size = 20),
        axis.text = element_text(size = 20),
        legend.title = element_text(size = 20),
        legend.text = element_text(size = 20)) 

p8

#png("./figures/network_distributions.png", bg = "white", width =3600, height = 1000, units = "px", res = 150)
png(filename = "./__cache__/figures3.png",  bg = "transparent", width =3600, height = 1000, units = "px", res = 150)
ggarrange(p7, NULL, NULL, p8, 
          #labels = c("A", "B", "C"),
          ncol = 4, nrow = 1, align = "h", 
          common.legend = TRUE, legend = "bottom", widths = c(1,.8,.8,1))

Chi-sq Test

chisq.test(df.c1$count, df.c2$count, simulate.p.value = T, p = noi_stats$N)

## 
##  Pearson's Chi-squared test with simulated p-value (based on 2000
##  replicates)
## 
## data:  df.c1$count and df.c2$count
## X-squared = 58.333, df = NA, p-value = 0.02449

RL vs IBL Project Analysis(Up Sampling)

Analysis info and important parameters

Load subject data

Create the Group-Level Regressor Matrix \(X\)

Define the Networks

Quality and Characteristics of \(X\) and \(Y\)

Collinearity of Connectivity Regressors \(X\)

Distribution of Classes

Machine-Learning with Lasso

Cross-Validation

Examining the Predictive Connectome

Model Evaluation

Predicted vs. Observed

ROC

ROC Curve By Sliding Threshold

Stability of Estimated Beta Weights

Statistical analysis of Network Distribution

Nested Cross-Validation

Predicted vs. Observed

ROC

ROC By Sliding Threshold

Examining the Predictive Connectome

Stability of Estimated Beta Weights

Testing the validity of the Lasso model

Ablation test

Variance Inflation Factor

Brain Network Analysis (Power)

A Matrix

W Matrix

iGraph: Density

iGraph: Diameter

iGraph: Betweeness (Closeness)

iGraph: Distances

iGraph: Assortativity

W in Brain connection

Distribution of connections